'MiscMetabar' package | MiscMetabar-package |
Plot accumulation curves for 'phyloseq-class' object | accu_plot |
Plot accumulation curves with balanced modality and depth rarefaction | accu_plot_balanced_modality |
Compute the number of sequence to obtain a given proportion of ASV in accumulation curves | accu_samp_threshold |
Add information from 'blast_pq()' to the 'tax_table' slot of a _phyloseq_ object | add_blast_info |
Add dna in 'refseq' slot of a 'physeq' object using taxa names and renames taxa using prefix_taxa_names and number (default Taxa_1, Taxa_2 ...) | add_dna_to_phyloseq |
Add information about Guild for FUNGI the FUNGuild databse | add_funguild_info |
Add information to sample_data slot of a phyloseq-class object | add_info_to_sam_data |
Add new taxonomic rank to a phyloseq object. | add_new_taxonomy_pq |
Permanova on a phyloseq object | adonis_pq |
Permanova (adonis) on permutations of rarefaction even depth | adonis_rarperm_pq |
List the size of all objects of the GlobalEnv. | all_object_size |
Run ANCOMBC2 on phyloseq object | ancombc_pq |
Test if the mean number of sequences by samples is link to the modality of a factor | are_modality_even_depth |
Transform the otu_table of a 'phyloseq-class' object into a 'phyloseq-class' object with a binary otu_table. | as_binary_otu_table |
Visualization of two samples for comparison | biplot_pq |
Blast all sequence of 'refseq' slot of a 'phyloseq-class' object against a custom database. | blast_pq |
Blast some sequence against sequences from of a 'derep-class' object. | blast_to_derep |
Blast some sequence against 'refseq' slot of a 'phyloseq-class' object. | blast_to_phyloseq |
Build phylogenetic trees from refseq slot of a phyloseq object | build_phytree_pq |
Detect for chimera taxa using vsearch | chimera_detection_vs |
Search for a list of sequence in an object to remove chimera taxa using vsearch | chimera_removal_vs |
Plot OTU circle for 'phyloseq-class' object | circle_pq |
Clean phyloseq object by removing empty samples and taxa | clean_pq |
Compare samples in pairs using diversity and number of ASV including shared ASV. | compare_pairs_pq |
Count sequences in fasta or fastq file | count_seq |
Remove primers using cutadapt | cutadapt_remove_primers |
Fungal OTU in phyloseq format | data_fungi |
Fungal OTU in phyloseq format | data_fungi_mini |
Fungal OTU in phyloseq format | data_fungi_sp_known |
Compute different functions for different class of vector. | diff_fct_diff_class |
Compute paired distances among matrix (e.g. otu_table) | dist_bycol |
Calculate ecological distance among positive controls vs distance for all samples | dist_pos_control |
Distribution of sequences across a factor for one taxon | distri_1_taxa |
Translates a factor into colors. | fac2col |
Filter undesirable taxa using blast against a custom database. | filter_asv_blast filter_taxa_blast |
A wrapper of the function 'dada2::filterAndTrim()' to use in targets pipeline | filter_trim |
Create a visualization table to describe taxa distribution across a modality | formattable_pq |
Assign Guilds to Organisms Based on Taxonomic Classification | funguild_assign |
Funky palette color | funky_color |
Get the extension of a file | get_file_extension |
Retrieve the FUNGuild database | get_funguild_db |
Alluvial plot for taxonomy and samples factor vizualisation | ggaluv_pq |
Box/Violin plots for between-subjects comparisons of Hill Number | ggbetween_pq |
Scatterplot with marginal distributions and statistical results against Hill diversity of phyloseq object | ggscatt_pq |
Venn diagram of 'phyloseq-class' object using 'ggVennDiagram::ggVennDiagram' function | ggvenn_pq |
Automated model selection and multimodel inference with (G)LMs for phyloseq | glmutli_pq |
Performs graph-based permutation tests on phyloseq object | graph_test_pq |
Heat tree from 'metacoder' package using 'tax_table' slot | heat_tree_pq |
Graphical representation of hill number 0, 1 and 2 across a factor | hill_pq |
Test multiple times effect of factor on Hill diversity with different rarefaction even depth | hill_test_rarperm_pq |
Calculate hill number and compute Tuckey post-hoc test | hill_tuckey_pq |
iNterpolation and EXTrapolation of Hill numbers (with iNEXT) | iNEXT_pq |
Test if cutadapt is installed. | is_cutadapt_installed |
Test if falco is installed. | is_falco_installed |
Test if krona is installed. | is_krona_installed |
Test if mumu is installed. | is_mumu_installed |
Test if swarm is installed. | is_swarm_installed |
Test if vsearch is installed. | is_vsearch_installed |
Make Krona files using KronaTools. | krona |
Compute and test local contributions to beta diversity (LCBD) of samples | LCBD_pq |
List fastq files | list_fastq_files |
Post Clustering Curation of Amplicon Data. | lulu |
Lulu reclustering of class 'physeq' | lulu_pq |
Merge Krona files using KronaTools. | merge_krona |
Merge samples by a sample variable or factor | merge_samples2 merge_samples2,otu_table-method merge_samples2,phyloseq-method merge_samples2,sample_data-method |
Merge taxa in groups (vectorized version) | merge_taxa_vec merge_taxa_vec,otu_table-method merge_taxa_vec,phylo-method merge_taxa_vec,phyloseq-method merge_taxa_vec,taxonomyTable-method merge_taxa_vec,XStringSet-method |
Deprecated function(s) in the MiscMetabar package | adonis_phyloseq biplot_physeq clean_physeq ggVenn_phyloseq hill_phyloseq hill_tuckey_phyloseq lulu_phyloseq MiscMetabar-deprecated otu_circle physeq_graph_test physeq_heat_tree plot_deseq2_phyloseq plot_edgeR_phyloseq read_phyloseq sankey_phyloseq summary_plot_phyloseq venn_phyloseq write_phyloseq |
Visualization of a collection of couples of samples for comparison | multi_biplot_pq |
Test and plot multipatt result | multipatt_pq |
Multiple plot function | multiplot |
Plot taxonomic distribution across 3 taxonomic levels and optionally one sample factor | multitax_bar_pq |
MUMU reclustering of class 'physeq' | mumu_pq |
Normalize OTU table using samples depth | normalize_prop_pq |
Convert a value (or a fraction x/y) in percentage | perc |
Convert phyloseq OTU count data into DGEList for edgeR package | phyloseq_to_edgeR |
Return a DNAStringSet object from either a character vector of DNA sequences or the 'refseq' slot of a phyloseq-class object | physeq_or_string_to_dna |
Plot ANCOMBC2 result for phyloseq object | plot_ancombc_pq |
Plot DESeq2 results for a phyloseq or a DESeq2 object. | plot_deseq2_pq |
Plot edgeR results for a phyloseq or a edgeR object. | plot_edgeR_pq |
Plot information about Guild from tax_table slot previously created with 'add_funguild_info()' | plot_guild_pq |
Plot and test local contributions to beta diversity (LCBD) of samples | plot_LCBD_pq |
Plot the result of a mt test 'phyloseq::mt()' | plot_mt |
Plot species contributions to beta diversity (SCBD) of samples | plot_SCBD_pq |
Plot taxonomic distribution in function of a factor with stacked bar in % | plot_tax_pq |
Plot a tsne low dimensional representation of a phyloseq object | plot_tsne_pq |
Plot the partition the variation of a phyloseq object | plot_var_part_pq |
Recluster sequences of an object of class 'physeq' or a list of DNA sequences | asv2otu postcluster_pq |
Build a sample information tibble from physeq object | psmelt_samples_pq |
Rarefy (equalize) the number of samples per modality of a factor | rarefy_sample_count_by_modality |
Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format. | read_pq |
Rename the samples of a phyloseq slot | rename_samples |
Rename samples of an otu_table | rename_samples_otu_table |
Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object | reorder_taxa_pq |
Ridge plot of a phyloseq object | ridges_pq |
rotl wrapper for phyloseq data | rotl_pq |
Load sample data from file and rename samples using names of samples and an optional order | sample_data_with_new_names |
Sankey plot of 'phyloseq-class' object | sankey_pq |
A wrapper of write_pq to save in all three possible formats | save_pq |
Search for exact matching of sequences | search_exact_seq_pq |
Select one sample from a physeq object | select_one_sample |
Select a subset of taxa in a specified order where possible | select_taxa select_taxa,otu_table,character-method select_taxa,phylo,character-method select_taxa,phyloseq,character-method select_taxa,sample_data,character-method select_taxa,taxonomyTable,character-method select_taxa,XStringSet,character-method |
Filter ancombc_pq results | signif_ancombc |
Simplify taxonomy by removing some unused characters such as "k__" | simplify_taxo |
Scaling with ranked subsampling (SRS) curve of phyloseq object | SRS_curve_pq |
Subsample a fastq file copying the n_seq first sequences in a given folder | subsample_fastq |
Subset samples using a conditional boolean vector. | subset_samples_pq |
Subset taxa using a conditional named boolean vector. | subset_taxa_pq |
Subset taxa using a taxa control or distribution based method | subset_taxa_tax_control |
Summarize a 'phyloseq-class' object using a plot. | summary_plot_pq |
Re-cluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using SWARM | swarm_clustering |
Plot the distribution of sequences or ASV in one taxonomic levels | tax_bar_pq |
Make a datatable with the taxonomy of a 'phyloseq-class' object | tax_datatable |
Force taxa to be in columns in the otu_table of a physeq object | taxa_as_columns |
Force taxa to be in columns in the otu_table of a physeq object | taxa_as_rows |
Show taxa which are present in only one given level of a modality | taxa_only_in_one_level |
Summarize information from sample data in a table | tbl_sum_samdata |
This tutorial explores the dataset from Tengeler et al. (2020) available in the 'mia' package. obtained using 'mia::makePhyloseqFromTreeSE(Tengeler2020)' | Tengeler2020_pq |
Track the number of reads (= sequences), samples and cluster (e.g. ASV) from various objects including dada-class and derep-class. | track_wkflow |
Track the number of reads (= sequences), samples and cluster (e.g. ASV) for each sample | track_wkflow_samples |
Adds transparency to a vector of colors | transp |
Plot treemap of 2 taxonomic levels | treemap_pq |
Compute tSNE position of samples from a phyloseq object | tsne_pq |
Get the unique value in x or NA if none | unique_or_na |
Make upset plot for phyloseq object. | upset_pq |
Test for differences between intersections | upset_test_pq |
Partition the Variation of a phyloseq object by 2, 3, or 4 Explanatory Matrices | var_par_pq |
Partition the Variation of a phyloseq object with rarefaction permutations | var_par_rarperm_pq |
Venn diagram of 'phyloseq-class' object | venn_pq |
Verify the validity of a phyloseq object | verify_pq |
Search for a list of sequence in a fasta file against physeq reference sequences using vsearch | vs_search_global |
Recluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using vsearch software | vsearch_clustering |
Save phyloseq object in the form of multiple csv tables. | write_pq |